 (ns cljam.pileup
   (:require [clojure.string :refer [join]]
-            (cljam [sorter :as sorter])))
+            [cljam [cigar :as cgr]
+                   [sorter :as sorter]]))
 
 (defn substantial-seq [aln]
   (let [{seq :seq, cigar :cigar} aln]

    (let [[aln & rst] alns2]
      (if (or (nil? aln) (not= rname (:rname aln)) (< pos (:pos aln)))
        val
        (if (< pos (+ (:pos aln) (count (substantial-seq aln))))
          (recur rst (inc val))
          (recur rst val))))))


             {:rname rname, :pos pos, :n val}
             (if-not (or (nil? rst) (= rname (:rname (first rst))))
               (pileup* rst (:rname (first rst)) (:pos (first rst)))
               (if (< pos (+ (:pos aln) (cgr/count-ref (:cigar aln))))
                 (pileup* alns rname (inc pos))
                 (pileup* rst rname (inc pos)))))))))))

